Identification and estimation of the proportion of limiting cell types involved in the phytohemagglutinin response by limiting cell dose-response analysis

Fluoresceinated peanut agglutinin (PNA-FITC) and a monoclonal anti-T-cell antibodies were used to identify human thymocyte subpopulations. The phenotypes of PNA+ and PNA? thymocytes were studied using two different techniques: agglutination with PNA and double-labeling immunofluorescence. The mitogen-responsive PNA- subset was shown to include early thymocytes bearing the OKT9 antigen as well as lymphocytes with the OKT3 phenotype. Nearly all PNA+ thymocytes were found to bind simultaneously OKT4, OKT6, and OKT8 antibodies, whereas about 30% of them weakly bind the OKT3 antibody. These data suggest the existence of several intermediate stages of intrathymic differentiation, including a subset simultaneously bearing the OKT6- and OKT3-defined antigens.     

Conjugates of PNA with naphthalene diimide derivatives having a broad range of DNA affinities

Peptide nucleic acids (PNAs) are neutral DNA analogues, which bind single-stranded DNA (ssDNA) strongly and with high sequence specificity. However, binding efficiency is dependent on the purine content of the PNA strand. This property make more difficult application of PNA as hybridization probes in, e.g., PNA chips, since at a set temperature the hybridization of a fraction of the DNA targets to the PNA probes does not obey Watson-Crick binding rules. The polypurine PNAs, for example, bind the mismatch containing DNA targets stronger, than the pyrimidine rich PNAs their fully complementary targets. Herein we show that PNA-DNA binding efficiency can be finely tuned by the conjugation of derivatives of naphthalene diimide (NADI) to the N-terminus of PNA using polyamide linkers of different lengths. This approach can potentially be used for the design of PNA probes, which bind their DNA targets with similar affinity independently of the PNA sequence.     

Strand displacement recognition of mixed adenine-cytosine sequences in double stranded DNA by thymine-guanine PNA (peptide nucleic acid).

Mixed pyrimidine-purine peptide nucleic acids (PNAs) composed of thymines and guanines are shown to form a PNA(2)-DNA triplex with Watson-Crick complementary adenine-cytosine oligonucleotides and to bind complementary adenine-cytosine targets in double stranded DNA by helix invasion. These results for the first time demonstrate binding of an unmodified PNA oligomer to a mixed pyrimidine-purine target in double stranded DNA and illustrate a novel binding mode of PNA.     

Polynitroxyl albumin plus tempol attenuates liver injury and inflammation after hepatic ischemia and reperfusion

PNA+Tempol, albumin containing conjugated (polynitroxyl albumin; PNA) and free (4-hydroxyl-2,2,6,6-tetramethyl-piperidinyl-1-oxyl; Tempol) nitroxide may protect against injury caused by reactive oxygen species. Therefore, the actions of PNA+Tempol on liver injury and inflammation induced by hepatic ischemia and reperfusion (I/R) were examined. Rats were subjected to 1 h ischemia followed by 24 h reperfusion in the absence (I/R) or presence of PNA+Tempol (25%; 15 mL/kg, i.v.) (I/R+PNA+Tempol) or human serum albumin (23%; 13.5 mL/kg, i.v.) (I/R+HSA). Test solutions were administered prior to and for 2 h during reperfusion. Sham-operated rats underwent surgery with neither ischemia nor infusion. I/R+PNA+Tempol rats had significantly less liver injury and inflammation than I/R rats. I/R+PNA+Tempol livers exhibited focal lesions whereas I/R livers exhibited global necrosis. Likewise, plasma ALT activity was significantly lower in I/R+PNA+Tempol rats. PNA+Tempol reduced I/R-induced neutrophil accumulation and intercellular adhesion molecule-1 (ICAM-1) expression. HSA did not alter I/R-induced liver injury or inflammation. Sham-operated rats exhibited normal liver morphology and no inflammation. Attenuation of I/R liver injury by PNA+Tempol may be mediated by its effect on inflammation, the major contributor to I/R injury. Reduction of inflammation by PNA+Tempol is most likely due to the antioxidative nature of the nitroxides.     

The first synthesis of chiral PNA monomer-cyclen conjugates.

A synthetic route to novel chiral PNA monomer-cyclen conjugates was described for the first time, the targeted products were obtained in high yields under mild reaction conditions. The preliminary results demonstrated that the uracil-PNA monomer-cyclen conjugates can rapidly bind Zn2+ in aqueous solution, and the structure of the Zn(II) complex was confirmed facilely by HRMS spectra, 1H NMR spectra and elemental analysis.     

The human lymph node germinal center cell: characterization and isolation by using two-color flow cytometry

The germinal center of lymphoid tissues is a critical microenvironmental site of B cell activation and differentiation in response to antigenic stimuli. However, characterization of germinal center cells (GCC) in tissue sections has proved technically difficult. Therefore, we have employed two-color flow cytometric analysis of suspended human tonsillar lymphocytes in order to define more precisely the immunologic features of GCC. These cells were identified in suspension by virtue of their specific surface binding of the lectin peanut agglutinin (PNA), confirmed by tissue immunoperoxidase studies. Phycoerythrin-labeled lectin was used in combination with a variety of fluorescein-labeled antibodies in order to identify subpopulations of tonsillar lymphocytes. The majority of PNA+ cells were B cells, and both PNA+ and PNA- B cells stained for surface immunoglobulin light chains. PNA+ cells lacked surface IgD, but included cells with surface IgG and IgM. Both PNA+ and PNA- cells stained for B1, B2, BA-1, Leu-12, Leu-14, CR-I, and HLA-DR antigens, whereas CALLA was present only on PNA+ cells. There were differences between PNA+ and PNA- cells in the relative expression of B1 and B2 antigens, possibly reflecting differences in B cell activation or maturation. A small proportion of T cells were PNA+, including both helper/inducer and suppressor/cytotoxic phenotypes. PNA+ cells included both small and large lymphoid cells, and almost all DNA synthetic activity was associated with the large PNA+ cells. PNA+ B cells isolated by cell sorting had morphologic features characteristic of GCC. Therefore, PNA+ cells in suspension appeared to represent GCC, and features of these cells that cannot be convincingly shown in tissue section studies were demonstrated by flow cytometry.     

Cellular remodeling of HCO3(-)-secreting cells in rabbit renal collecting duct in response to an acidic environment

The renal cortical collecting duct (CCD) consists of principal and intercalated cells. Two forms of intercalated cells, those cells involved in H+/HCO3- transport, have recently been described. H+-secreting cells are capable of apical endocytosis and have H+ATPase on the apical membrane and a basolateral Cl-/HCO3- exchanger. HCO3(-)-secreting cells bind peanut agglutinin (PNA) to apical membrane receptors and have diffuse or basolateral distribution of H+ATPase; their Cl-/HCO3- exchanger is on the apical membrane. We found that 20 h after acid feeding of rabbits, there was a fourfold increase in number of cells showing apical endocytosis and a numerically similar reduction of cells binding PNA. Incubation of CCDs at pH 7.1 for 3-5 h in vitro led to similar, albeit less pronounced, changes. Evidence to suggest internalization and degradation of the PNA binding sites included a reduction in apical binding of PNA, decrease in pH in the environment of PNA binding, and incorporation of electron-dense PNA into cytoplasmic vesicles. Such remodeling was dependent on protein synthesis. There was also functional evidence for loss of apical Cl-/HCO3- exchange on PNA-labeled cells. Finally, net HCO3- flux converted from secretion to absorption after incubation at low pH. Thus, exposure of CCDs to low pH stimulates the removal/inactivation of apical Cl-/HCO3- exchangers and the internalization of other apical membrane components. Remodeling of PNA-labeled cells may mediate the change in polarity of HCO3- flux observed in response to acid treatment.     

Cadmium and calcium uptake in isolated mitochondria-rich cell populations from the gills of the freshwater rainbow trout

A novel cell isolation technique was used to characterize cadmium and calcium uptake in distinct populations of gill cells from the adult rainbow trout (Oncorhynchus mykiss). A specific population of mitochondria-rich (MR) cell, termed the PNA+ MR cell (PNA is peanut lectin agglutinin), was found to accumulate over threefold more 109Cd than did PNA- MR cells, pavement cells (PV cells), and mucous cells during a 1-h in vivo exposure at 2.4 microg/l 109Cd. In vitro 109Cd exposures, performed in standard PBS and Cl- -free PBS, at concentrations from 1 to 16 microg/l 109Cd, were also carried out to further characterize Cd2+ uptake kinetics. As observed during in vivo experiments, PNA+ MR cells accumulated significantly more 109Cd than did other cell types when exposures were performed by an in vitro procedure in PBS. Under such conditions, Cd2+ accumulation kinetics in all cell types could be described with Michaelis-Menten relationships, with Km values of approximately 3.0 microg/l Cd (27 nM) for both MR cell subtypes and 8.6 microg/l Cd (77 nM) for PV cells. In similar experiments performed in Cl- -free conditions, a significant reduction in 109Cd accumulation in PNA+ MR cells was seen but not in PNA- MR or in PV cells. In vitro 45Ca fluxes were also performed to determine the cellular localization of Ca2+ transport in these functionally distinct populations of gill cells. 45Ca uptake was most pronounced in PNA+ MR cells, with levels over threefold higher than those found in either PNA(-) MR or in PV cells. Results from the present study suggest that the PNA+ MR cell type is a high-affinity and high-capacity site for apical entry of Cd2+ and Ca2+ in the gill epithelium of rainbow trout.     

PNA technology

Peptide nucleic acids (PNA) are deoxyribonucleic acid (DNA) mimics with a pseudopeptide backbone. PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion. Therefore, these molecules are of interest in many areas of chemistry, biology, and medicine, including drug discovery, genetic diagnostics, molecular recognition, and the origin of life. Recent progress in studies of PNA properties and applications is reviewed.     

肽核酸—基因调控的利器

肽核酸(PNA)是具有类多肽骨架的DNA类似物,PNA的主链骨架是由N(2-氨基乙基)-甘氨酸与核酸碱基通过亚甲基羰基连接而成的。PNA可以特异性地与DNA或RNA杂交,形成稳定的复合体。PNA由于其自身的特点可以对DNA复制、基因转录、翻译等进行有针对的调控,同时作为杂交探针大大提高了遗传学检测和医疗诊断的效率和灵敏度。肽核酸（PNA）特异性地识别和结合互补核酸序列被引进用于医学和生物学的研究,展示了其独特的生化属性,成为了基因奥秘的探索者。     

肽核酸的分子生物学效应及应用

肽核酸(PNA)是一类以酰胺键连接骨架替代核酸中核糖磷酸二酯键骨架构成的核酸类似物,其中N-乙基甘氨酸骨架PNA与核酸链以Waston-Crick碱基配对形式稳定互补结合,具有广泛生物学效应,包括调节DNA识别蛋白质的功能以及调节转录和翻译.在分子生物学研究中PNA作为新的工具在多方面得到应用.除它的DNA(RNA)结合特性外PNA在生物稳定性、细胞摄取、结构修饰多方面的研究进展显示出作为基因调节药物具有良好前景.     

PNA zipper as a dimerization tool: Development of a bZip mimic

The article describes the use of a PNA duplex (PNA zipper) as a tool to dimerize or bring in close proximity two polypeptides or protein domains. The amino acid sequence to be dimerized is covalently bound to complementary PNA sequences. Annealing of the PNA strands results in dimer formation. To test the ability of the “PNA‐zipper” as a dimerization tool, we designed a GCN4 mimetic, where the leucine‐zipper dimerization domain was replaced by the PNA zipper, whereas the basic DNA‐binding domain was covalently attached to the PNA. The molecule was assembled by chemical ligation of the peptide corresponding to the DNA‐binding domain of GCN4 modified with a succinyl thioester with two complementary PNAs harboring a cysteine residue. Electromobility‐shift experiments show the ability of the PNA zipper‐GCN4 to bind selected DNA duplexes. The PNA zipper‐GCN4 binds both the TRE and CRE DNA sites, but it does not bind TRE and CRE mutants containing even a single base mutation, as the native GCN4. The ability to fold upon complexation with DNA was investigated by CD. A good correlation between the ability of the PNA zipper‐GCN4 to fold into α helices and the ability to bind DNA was found. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 434–441, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Crystal structures of the PNA-porphyrin complex in the presence and absence of lactose: mapping the conformational changes on lactose binding, interacting surfaces, and supramolecular aggregations

The extraordinary recognition specificity of lectins for carbohydrate ligands appears to be violated as they also bind to porphyrins and other noncarbohydrate ligands. In this study, crystal structures of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) bound to peanut agglutinin (PNA) in the presence and absence of lactose were determined. The binding of H(2)TPPS with PNA involved 11 molecules of H(2)TPPS in different supramolecular stacking arrangements associated with a tetramer of PNA in the crystals of the PNA-H(2)TPPS binary complex as well as the PNA-H(2)TPPS-lactose ternary complex. The ternary complex involved lactose binding only to two subunits of the PNA tetramer, which did not have porphyrin interacting in the vicinity of the carbohydrate-binding site. Comparison of the two structures highlighted the plasticity of the carbohydrate-binding site expressed in terms of the conformational change in lactose binding. The unusual quaternary structure of PNA, which results in exposed protein-protein interaction sites, might be responsible for the porphyrin binding. The association of porphyrin in diverse oligomeric stacking arrangements observed in the PNA-H(2)TPPS complex suggested the possibility of protein-porphyrin aggregation under abnormal physiological conditions. The structures described here provide a possible native conformation of the carbohydrate-binding site of PNA in the absence of the ligand, highlight mapping of the unsaturated binding surfaces of PNA using porphyrin interactions, indicate new leads toward possible application of this lectin in photodynamic therapy, and exhibit diverse modes of porphyrin-lectin interactions with implications to porphyria, a disease that results from abnormal accumulation of porphyrins.     

Thymic lymphocytes. III. Cooperative phenomenon in the proliferation of thymocytes under Con A stimulation

In the present paper, the response of thymocytes to Con A is analyzed in terms of a cooperative phenomenon between medullary thymocytes, cortical thymocytes, thymic accessory cells, and interleukin 2. Medullary thymocytes respond spontaneously to Con A and produce IL-2. The addition of exogenously produced IL-2 enhances their proliferation. Small numbers of cortical (PNA+) thymocytes do not respond to Con A, even in the presence of IL-2-containing supernatant. By increasing the number of PNA+ cells per well, sensitivity to Con A and IL-2 appears. This response may be linked either to the increase in a minor PNA+-responding population and/or to the enhanced contamination by medullary thymocytes and macrophages in non-responding PNA+ thymocyte population. In this hypothesis, either the contaminating cells respond by themselves and/or cooperate with PNA+ cells to induce their proliferation. Coculture of non-responding low numbers of PNA+ thymocytes with Con A- and IL-2-containing supernatant in the presence of PNA- cells containing thymic medullary thymocytes and macrophages always produces a higher response than that of each individual population. These results show that a cooperative phenomenon occurs in the cocultures of PNA+ and PNA- thymic cells. We can show using PNA+ and PNA- thymocytes with different Thy 1 alleles, that indeed both PNA+ and populations participate PNA-thymocytes with different Thy 1 alleles, that indeed both PNA+ and PNA- populations participate in the generation of proliferating cells. We can demonstrate, by lysis experiments with monoclonal antibodies and complement that at the end of coculture, most of the proliferating cells are Lyt 1+, and part are Lyt 2+ or L3T4+. We discuss the fact that the phenotype of the cells after activation does not allow us to deduce the phenotype of their precursors. Lysis of Ia+ cells prior to coculture, reduces the level of the proliferative response but does not modify the percentage of cooperation produced by the coculture. Cooperation with medullary mature thymocytes or the presence of active Ia- accessory cells possibly able to convert to Ia expression during coculture experiments may account for these results.     

Dexamethasone induces different cellular protein synthetic responses in PNA+ and PNA- mouse thymocyte subpopulations

Thymocytes from adrenalectomized BALB/c male mice were separated by peanut agglutination (PNA) into cortical, corticosensitive, PNA+ cells and larger, medullary, corticoresistant, PNA- cells; the extent of cross-contamination of PNA+ and PNA- cells, and vice versa, was checked by flow microfluorometry. Glucocorticoid receptor profiles were established with 3H-dexamethasone as probe; no differences in receptor affinity or cellular concentration, or in cytoplasmic and nuclear compartmentalization were seen between PNA+ and PNA- cells. On two-dimensional gel electrophoresis, PNA+ and PNA- thymocytes from oil-injected (control) adrenalectomized mice showed patterns of incorporation of 35S-methionine into protein that differed in at least 12 spots, as revealed by autoradiography. PNA+ and PNA- cells from mice treated with submaximal (6 micrograms/day) or near-maximal thymolytic doses of dexamethasone (20 micrograms/day) were also examined by two-dimensional gel electrophoresis. Both PNA+ and PNA- cells showed substantial, overlapping dexamethasone-induced changes in protein synthetic profiles.     

Quinoxaline antibiotics enhance peptide nucleic acid binding to double-stranded DNA

The effects of a wide range of DNA binding drugs on peptide nucleic acid (PNA) binding to double-stranded DNA by strand displacement have been investigated using a gel retardation assay. The bis-PNA [H-(Lys)-TTJTTJTTTT-(eg)(3)-TTTTCTTCTT-Lys-NH(2)] was used together with a 248 bp DNA fragment containing an appropriate target for the PNA. Most of the ligands that were studied, including DNA minor groove binders as well as intercalators and bis-intercalators, either have no effect or strongly inhibit PNA binding to DNA. By contrast, quinoxaline antibiotics facilitate PNA-DNA complex formation. The "PNA-helper" effect of echinomycin was studied in more detail using time and temperature dependence experiments to elucidate the mechanism. PNA binding to DNA follows pseudo-first-order kinetics, but the initial rate of binding is accelerated more than 10-fold in the presence of 10 microM echinomycin. The activation energy for PNA binding to dsDNA is lowered 2-fold by the antibiotic (45 vs 90 kJ/mol in the control). The reasons why quinoxalines promote the binding of PNA to DNA are not entirely clear but may well include distortions (opening) of the double helix that facilitate PNA invasion. This study establishes that the efficacy of DNA-targeted PNA antigene molecules could potentially be enhanced by judiciously adding certain DNA-interactive ligands.